title: Characterization of Pythium Transcriptome and Gene Expression Analysis at Different Stages of Fermentation.
abstract: The Pythium splendens is a potentially useful organism for the synthesis of large amounts of eicosapentaenoic acid. Peak biomass and lipid accumulation do not occur at the same time and growth temperature has an effect on the fatty acid composition. Little is known about the pathway or the genes involved in growth, lipid synthesis or temperature resistance in P. splendens. Analysis of the transcriptome and expression profile data for P.splendensRBB-5 were used to extend genetic information for this strain and to contribute to a comprehensive understanding of the molecular mechanisms involved in specific biological processes.
  
  
  
  This study used transcriptome assembly and gene expression analysis with short-read sequencing technology combined with a tag-based digital gene expression (DGE) system. Assembled sequences were annotated with gene descriptions, such as gene ontology (GO), clusters of orthologous group (COG) terms and KEGG orthology (KO) to generate 23,796 unigenes. In addition, we obtained a larger number of genes at different stages of fermentation (48, 100 and 148 h). The genes related to growth characteristics and lipid biosynthesis were analyzed in detail. Some genes associated with lipid and fatty acid biosynthesis were selected to confirm the digital gene expression (DGE) results by quantitative real-time PCR (qRT-PCR).
  
  
  
  The transcriptome improves our genetic understanding of P.splendensRBB-5 greatly and makes a large number of gene sequences available for further study. Notably, the transcriptome and DGE profiling data of P.splendensRBB-5 provide a comprehensive insight into gene expression profiles at different stages of fermentation and lay the foundation for the study of optimizing lipid content and growth speed at the molecular level.
authors.affiliation: Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China ; Key Laboratory of Molecular Biophysics Ministry of Education, Huazhong University of Science and Technology, Wuhan, China ; Wuhan Institute of Biotechnology, Wuhan, China.
authors.forename: Yuanmin
authors.initials: Y
authors.lastname: Zhu
authors.forename: Pengpeng
authors.initials: P
authors.lastname: Zhou
authors.forename: Jingrong
authors.initials: J
authors.lastname: Hu
authors.forename: Ruijiao
authors.initials: R
authors.lastname: Zhang
authors.forename: Liang
authors.initials: L
authors.lastname: Ren
authors.forename: Maoteng
authors.initials: M
authors.lastname: Li
authors.forename: Fan
authors.initials: F
authors.lastname: Ning
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Longjiang
authors.initials: L
authors.lastname: Yu
mesh_terms: D005285:Fermentation; D008401:Gas Chromatography-Mass Spectrometry; D020869:Gene Expression Profiling; D008055:Lipids / Q000032:analysis; D011775:Pythium / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D008055:Lipids